Reproducing the figures of the manuscript

Load libraries

library(qs)
library(Seurat)
library(tidyverse)
library(miloDE)
library(sessioninfo)
library(EnhancedVolcano)
library(pals)
library(scMisc)

Figure 1

UMAP of all cells (Figure 1B)

options(timeout = 3600)
if (!file.exists("umap_figure.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "umap_figure.qs"
    )
}
umap_figure <- qread("umap_figure.qs")
DimPlot(
    umap_figure,
    reduction = "umap.scvi.full",
    pt.size = .1,
    alpha = .1,
    cols = umap_figure@misc$cluster_col,
    label = TRUE,
    raster = FALSE
) +
    NoLegend() +
    theme(
        axis.text = element_blank(),
        axis.ticks = element_blank()
    ) +
    xlab("UMAP_1") +
    ylab("UMAP_2")

Figure 2

UMAP immune cells (Figure 2A)

options(timeout = 3600)
if (!file.exists("ic_figure.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "ic_figure.qs"
    )
}
ic_figure <- qread("ic_figure.qs")
DimPlot(
    ic_figure,
    reduction = "umap.rpca",
    pt.size = .1,
    alpha = .3,
    cols = ic_figure@misc$ic_cluster_col,
    label = TRUE,
    raster = FALSE
) +
    theme(
        axis.text = element_blank(),
        axis.ticks = element_blank()
    ) +
    NoLegend() +
    xlab("UMAP1") +
    ylab("UMAP2")

Feature plots immune cells (Figure 2B)

FeaturePlot(
    ic_figure,
    features = c("MS4A7", "CX3CR1", "TREM2", "LYVE1", "FOLR2", "TIMD4"),
    reduction = "umap.rpca",
    pt.size = 0.1,
    raster = FALSE,
    coord.fixed = TRUE,
    cols = c("#F0F0F0", "#CB181D"),
    order = TRUE,
    ncol = 3
) &
    theme(
        axis.text = element_blank(),
        axis.ticks = element_blank()
    ) &
    xlab("UMAP1") &
    ylab("UMAP2")

Enrichment of gene ontology terms in Macro 18 (Figure 2C)

options(timeout = 3600)
if (!file.exists("enrichr_macro18.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "b_plasma_figure.qs"
    )
}
enrichr_macro18 <- qread("enrichr_macro18.qs")
enrichr_macro18 |>
    dplyr::slice_min(order_by = Adjusted.P.value, n = 10, with_ties = FALSE) |>
    tidyr::separate(Overlap, into = c("overlap1", "overlap2")) |> # separate overlap in two columns
    dplyr::mutate(Term = gsub(x = Term, pattern = "\\s\\(.+\\)", replacement = "")) |>
    dplyr::mutate(overlap = as.numeric(overlap1) / as.numeric(overlap2)) |> # calculcate overlap
    ggplot(aes(y = reorder(Term, -log10(Adjusted.P.value)), x = -log10(Adjusted.P.value))) +
    geom_col(fill = scales::hue_pal()(5)[1]) +
    labs(
        x = "-Log10 Adjusted P value",
        y = ""
    ) +
    theme_classic() +
    theme(legend.position = "none")

Dot plot IGH chain genes (Figure 2E)

options(timeout = 3600)
if (!file.exists("ic_figure.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "b_plasma_figure.qs"
    )
}
b_plasma_figure <- qread("b_plasma_figure.qs")
DotPlot(
    b_plasma_figure,
    features = c("IGHM", "IGHD", "IGHG1", "IGHG2", "IGHG3", "IGHG4", "IGHA1", "IGHA2"),
    scale = FALSE,
    dot.scale = 10
) +
    viridis::scale_color_viridis(option = "viridis") +
    theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5, face = "italic")) +
    xlab("") +
    ylab("")

Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.

Figure 3

Propeller abundance PNP vs CTRL (Figure 3A)

options(timeout = 3600)
if (!file.exists("propeller_PNP_CTRL.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "propeller_PNP_CTRL.qs"
    )
}
if (!file.exists("propeller_PNP_CTRL.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "propeller_PNP_CTRL_ic.qs"
    )
}
propeller_PNP_CTRL <- qread("propeller_PNP_CTRL.qs")
propeller_PNP_CTRL_ic <- qread("propeller_PNP_CTRL_ic.qs")

# function to plot custom dotplot
dotplotPropeller <- function(data, color, title) {
    ggplot(data, aes(x = log2ratio, y = fct_reorder(cluster, log2ratio), color = cluster)) +
        geom_point(size = 5) +
        theme_classic() +
        geom_vline(
            xintercept = 0, color = "red",
            linetype = "solid"
        ) +
        scale_color_manual(values = color) +
        xlab("Log2 fold change") +
        ylab(NULL) +
        theme(legend.position = "none") + 
        ggtitle(title)
}
dotplotPropeller(propeller_PNP_CTRL, color = umap_figure@misc$cluster_col, title = "PNP vs CTRL main clusters")

dotplotPropeller(propeller_PNP_CTRL_ic, color = ic_figure@misc$ic_cluster_col, title = "PNP vs CTRL immune cells")

Covarying Neighborhood Analysis (Figure 3B)

options(timeout = 3600)
if (!file.exists("cna_pnp_gratio_figure.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "cna_pnp_gratio_figure.qs"
    )
}
if (!file.exists("cna_incat_figure.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "cna_incat_figure.qs"
    )
}
cna_pnp_gratio_figure <- qread("cna_pnp_gratio_figure.qs")
cna_incat_figure <- qread("cna_incat_figure.qs")

# function to plot CNA feature plot
fplotCNA <-  function(object, feature, title) {
    FeaturePlot(
        object,
        reduction = "umap.scvi.full",
        features = feature,
        pt.size = 0.1,
        order = FALSE,
        coord.fixed = TRUE,
        raster = FALSE,
        alpha = 0.2
    ) +
    scale_colour_gradient2(
        low = "#2166AC",
        mid = "white",
        high = "#B2182B",
        midpoint = 0,
    ) +
    theme(
        axis.text = element_blank(),
        axis.ticks = element_blank(),
    ) +
    labs(
        title = title, color = "Correlation", x = "UMAP1", y= "UMAP2"
    )
}

fplotCNA(cna_pnp_gratio_figure, "cna_ncorrs_pnp", title = "PNP")

Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.

fplotCNA(cna_incat_figure, "cna_ncorrs", title = "INCAT")

Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.

fplotCNA(cna_pnp_gratio_figure, "cna_ncorrs_gratio", title = "g-ratio")

Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.

Number of DEGs (Figure 3C)

options(timeout = 3600)
if (!file.exists("pnp_ctrl_pseudobulk_de.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "pnp_ctrl_pseudobulk_de.qs"
    )
}
pnp_ctrl_pseudobulk <- qread("pnp_ctrl_pseudobulk_de.qs")
pnp_ctrl_pseudobulk |>
    mutate(cluster = fct_reorder(cluster, n)) |>
    ggplot(aes(x = cluster, y = n, fill = cluster)) +
    geom_col() +
    coord_flip() +
    scale_fill_manual(values = umap_figure@misc$cluster_col) +
    theme_classic() +
    theme(legend.position = "none") +
    labs(
        x = "",
        y = "",
        title = "PNP vs CTRL"
    )

MiloDE DEGs PNP vs CTRL (Figure 3D)

options(timeout = 3600)
if (!file.exists("milo_figure.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "milo_figure.qs"
    )
}

milo_figure <- qread("milo_figure.qs")
plotMiloDE <- function(condition, title) {
    plot <- 
    plot_milo_by_single_metric(
        milo_figure$obj,
        milo_figure$stat[[condition]],
        colour_by = "n_DE_genes",
        layout = "UMAP.SCVI.FULL",
        size_range = c(0.5, 5),
        edge_width = c(0.1, 1.0),
        edge_weight.thres = 10
    ) +
    viridis::scale_fill_viridis(name = "# DE genes", option = "inferno") +
    ggtitle(title)
    print(plot)
}

plotMiloDE("pnp", "PNP vs CTRL")

Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.

Pseudobulk DE PNP vs CTRL (Figure 3E)

options(timeout = 3600)
if (!file.exists("de_pseudo_pnp_ctrl.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "de_pseudo_pnp_ctrl.qs"
    )
}
de_pseudo_pnp_ctrl <- qread("de_pseudo_pnp_ctrl.qs")

# volcano plot function
volcanoPlot <- function(cluster, input, FCcutoff = 2, selectLab = NULL, drawConnectors = TRUE, condition1, condition2) {
    input <- input[[cluster]]
    volcano <- EnhancedVolcano::EnhancedVolcano(
        data.frame(input),
        lab = paste0("italic('", input[["gene"]], "')"),
        x = "avg_logFC",
        y = "p_val_adj",
        xlim = c(min(input[["avg_logFC"]], max(input[["avg_logFC"]]))),
        ylim = c(0, max(-log10(input[["p_val_adj"]]))),
        pCutoff = 0.1,
        FCcutoff = FCcutoff,
        axisLabSize = 15,
        pointSize = 2,
        labSize = 5,
        subtitle = NULL,
        caption = NULL,
        border = "full",
        gridlines.major = FALSE,
        gridlines.minor = FALSE,
        drawConnectors = drawConnectors,
        lengthConnectors = unit(0.0001, "npc"),
        title = paste(condition1, "vs", condition2, "in ", cluster),
        boxedLabels = TRUE,
        selectLab = selectLab,
        xlab = bquote(~ Log[2] ~ "fold change"),
        ylab = bquote(~ -Log[10] ~ "adjusted p-value"),
        parseLabels = TRUE,
        legendLabels = c(
            "NS", "logFC",
            "p-val", "p-val + logFC"
        ),
        legendPosition = "right",
    )
}

# define clusters of interest
cluster_de <- c("mySC", "nmSC", "repairSC", "PC2")

# define genes of interests
lab_pnp_ctrl <- list(
    "mySC" = paste0("italic('", c("DCN", "TNXB", "COL1A1", "COL15A1", "CD53", "IL4R", "CD74"), "')"),
    "nmSC" = paste0("italic('", c("IL10RA", "IL13RA1", "CSF2RA", "TGFBI"), "')"),
    "repairSC" = paste0("italic('", c("GALR1", "TMEM47"), "')"),
    "PC2" = paste0("italic('", c("MFAP5", "NLGN4Y", "PCDH11Y", "IFIT3", "OASL", "MX1"), "')")
)

# plot volcano plots of selected clusters
purrr::walk(
    cluster_de,
    function(cluster) {
        print(volcanoPlot(
            cluster = cluster,
            input = de_pseudo_pnp_ctrl,
            FCcutoff = 2,
            condition1 = "PNP",
            condition2 = "CTRL",
            selectLab = lab_pnp_ctrl[[cluster]]
        ))
    }
)

Figure 4

Abundance of clusters per PNP subtype (Figure 4A)

options(timeout = 3600)
if (!file.exists("abundance_main_clusters.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "abundanance_main_clusters.qs"
    )
}
abundance_main_clusters <- qread("abundance_main_clusters.qs")

abundance_main_clusters |>
    ggplot() +
    geom_col(
        aes(x = type, y = count, fill = cell),
        color = "black",
        linewidth = 0.1,
        position = "fill"
    ) +
    scale_fill_manual(values = umap_figure@misc$cluster_col) +
    guides(fill = guide_legend(title = NULL)) +
    theme_classic() +
    ylab("Proportion of cells") +
    xlab("") +
    theme(axis.text.x = element_text(
        angle = 90,
        hjust = 1, vjust = 0.3
    ))

Propeller abundance of PNP subtypes main cluster (Figure 4B)

options(timeout = 3600)
if (!file.exists("propeller_PNP_subtypes_main.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "propeller_PNP_subtypes_main.qs"
    )
}

propeller_PNP_subtypes_main <- qread("propeller_PNP_subtypes_main.qs")
purrr::walk(
    c("VN", "CIDP", "CIAP"),
    function(condition) {
        print(dotplotPropeller(
            propeller_PNP_subtypes_main[[condition]],
            color = umap_figure@misc$cluster_col,
            title = paste0("CTRL vs ", condition, " main")
        ))
    }
)

Propeller abundance of PNP subtypes immune cluster (Figure 4C)

options(timeout = 3600)
if (!file.exists("propeller_PNP_subtypes_ic.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "propeller_PNP_subtypes_ic.qs"
    )
}
propeller_PNP_subtypes_ic <- qread("propeller_PNP_subtypes_ic.qs")
purrr::walk(
    c("VN", "CIDP", "CIAP"),
    function(condition) {
        print(dotplotPropeller(
            propeller_PNP_subtypes_ic[[condition]],
            color = umap_figure@misc$cluster_col,
            title = paste0("CTRL vs ", condition, " immune")
        ))
    }
)

Manual PTPRC quantif (Figure 4F)

options(timeout = 3600)
if (!file.exists("manual_xenium_quantification.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "manual_xenium_quantification.qs"
    )
}

manual_xenium_quantification <- qread("manual_xenium_quantification.qs")
plotQuanti <- function(y_value, title) {
    plot <- 
    manual_xenium_quantification |>
        ggplot(aes(x = level2, y = .data[[y_value]], fill = level2)) +
        geom_boxplot() +
        geom_jitter(height = 0, width = 0.1) +
        scale_fill_manual(values = umap_figure@misc$level2_cols) +
        guides(fill = guide_legend(title = NULL)) +
        theme_classic() +
        xlab("") +
        ylab("PTPRC density") +
        ggtitle(title) +
        theme(
            legend.position = "none",
            axis.text.x = element_text(
                angle = 90,
                hjust = 1,
                vjust = 0.3,
            )
        )
        print(plot)
}

purrr::walk2(
    c("endoPTPRC_density_sum", "epiPTPRC_density"),
    c("endoneurial", "epineurial"),  
    function(y_value, title) {
        plotQuanti(y_value = y_value, title = title)
    }
)

MiloDE DEGs PNP subtypes(Figure 4G)

purrr::walk2(
    c("vn", "cidp", "ciap"),
    c("VN vs CTRL", "CIDP vs CTRL", "CIAP vs CTRL"),
    function(condition, title) {
        plotMiloDE(condition, title)
    }
)

Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.

Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.

Supplementary Figure 1

Demographics plot (Figure S1A)

options(timeout = 3600)
if (!file.exists("demographics.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "demographics.qs"
    )
}

demographics <- qread("demographics.qs")

plotDemographics <- function(var) {
    plot <- demographics |>
        dplyr::filter(!is.na(.data[[var]])) |>
        ggplot(aes(x = level2, y = .data[[var]], fill = level2)) +
        geom_boxplot() +
        geom_point() +
        theme_bw() +
        scale_fill_manual(values = umap_figure@misc$level2_cols) +
        xlab("") +
        ylab("") +
        ggtitle(var) +
        theme(legend.position = "none")
    print(plot)
}

purrr::walk(c("age", "ncv_tibial_motoric", "incat"), plotDemographics)

demographics |>
    ggplot(aes(x = level2, fill = sex)) +
    geom_bar() + 
    theme_bw() +
    scale_fill_manual(values = pals::cols25(2)) +
    xlab("") +
    ylab("") +
    ggtitle("sex")

UMAP grouped by center and sample (Figure S1C)

DimPlot(
    umap_figure,
    reduction = "umap.scvi.full",
    pt.size = .1,
    raster = FALSE,
    alpha = 0.1,
    group.by = "center",
    cols = pals::cols25(3),
    label = FALSE
) +
    theme(
        axis.text = element_blank(),
        axis.ticks = element_blank()
    ) +
    xlab("UMAP_1") +
    ylab("UMAP_2")

my_cols_50 <- unname(Polychrome::createPalette(50, pals::cols25()))

DimPlot(
    umap_figure,
    reduction = "umap.scvi.full",
    pt.size = .1,
    raster = FALSE,
    alpha = 0.1,
    group.by = "sample",
    cols = umap_figure@misc$sample_cols,
    label = FALSE
) +
    theme(
        axis.text = element_blank(),
        axis.ticks = element_blank()
    ) +
    xlab("UMAP_1") +
    ylab("UMAP_2")

Number of genes per nucleus (Figure S1D)

count_genes <- dplyr::tibble(
    feature = umap_figure@meta.data$nFeature_RNA,
    sample = umap_figure@meta.data$sample
)

count_genes |>
    ggplot(aes(x = sample, y = feature, fill = sample)) +
    geom_boxplot() +
    scale_fill_manual(values = umap_figure@misc$sample_cols) +
    theme_classic() +
    theme(legend.position = "none") +
    xlab("") +
    ylab("") +
    ggtitle("Number of genes per nucleus") +
    theme(axis.text.x = element_text(angle = 90))

Abundance of clusters per sample (Figure S1E)

options(timeout = 3600)
if (!file.exists("abundance_main_clusters_sample.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "abundanance_main_clusters_sample.qs"
    )
}
abundance_main_clusters_sample <- qread("abundance_main_clusters_sample.qs")
abundance_main_clusters_sample |>
    mutate(type = factor(type, levels = rev(levels(factor(type))))) |>
    ggplot() +
    geom_col(
        aes(x = type, y = count, fill = cell),
        color = "black",
        linewidth = 0.1,
        position = "fill"
    ) +
    scale_fill_manual(values = umap_figure@misc$cluster_col) +
    theme_classic() +
    ylab("Proportion of cells") +
    xlab("") +
    theme(
        axis.text.x = element_text(
            angle = 90,
            hjust = 1, vjust = 0.3
        ),
        legend.position = "none"
    ) +
    coord_flip()

Supplementary Figure 2

Dotplot of main clusters(Figure S2A)

options(timeout = 3600)
if (!file.exists("dotplot_data.qs")) {
    download.file(
        "https://zenodo.org/records/14226219/files/umap_figure.qs?download=1",
        "abundanance_main_clusters_sample.qs"
    )
}
dotplot_data <- qread("dotplot_data.qs")

# Seurat DotPlot function (only ggplot part to avoid calculations)
DotPlotModified <- function(
  data.plot,
  cols = c("lightgrey", "blue"),
  dot.scale = 6,
  scale.by = 'radius',
  scale.min = NA,
  scale.max = NA
) {
  scale.func <- switch(
    EXPR = scale.by,
    'size' = scale_size,
    'radius' = scale_radius,
    stop("'scale.by' must be either 'size' or 'radius'")
  )
  color.by <- 'avg.exp.scaled'
  plot <- ggplot(data = data.plot, mapping = aes_string(x = 'features.plot', y = 'id')) +
    geom_point(mapping = aes_string(size = 'pct.exp', color = color.by)) +
    scale.func(range = c(0, dot.scale), limits = c(scale.min, scale.max)) +
    theme(axis.title.x = element_blank(), axis.title.y = element_blank()) +
    guides(size = guide_legend(title = 'Percent Expressed')) + 
    cowplot::theme_cowplot()
  plot <- plot + guides(color = guide_colorbar(title = 'Average Expression'))
  return(plot)
}

DotPlotModified(
    data.plot = dotplot_data,
    scale.by = "size"
) +
    viridis::scale_color_viridis(option = "viridis") +
    theme(axis.text.x = element_text(
        angle = 90,
        vjust = 0.5,
        hjust = 1,
        face = "italic",
        size = 7
        ),
        legend.position = "top",
        legend.text = element_text(size = 6),
        legend.title = element_text(size = 10)
        ) +
    xlab("") +
    ylab("")

Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.

Warning: Removed 688 rows containing missing values or values outside the scale range
(`geom_point()`).

Session info

session_info()

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.1 (2023-06-16)
 os       Ubuntu 22.04.5 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  C.UTF-8
 ctype    C.UTF-8
 tz       UTC
 date     2024-12-21
 pandoc   2.19.2 @ /usr/local/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package              * version    date (UTC) lib source
 abind                  1.4-5      2016-07-21 [1] RSPM (R 4.3.0)
 Augur                  1.0.3      2024-12-20 [1] Github (neurorestore/Augur@fa5d837)
 backports              1.4.1      2021-12-13 [1] RSPM (R 4.3.0)
 beachmat               2.18.0     2023-10-24 [1] Bioconductor
 beeswarm               0.4.0      2021-06-01 [1] RSPM (R 4.3.0)
 Biobase                2.62.0     2023-10-24 [1] Bioconductor
 BiocGenerics           0.48.1     2023-11-01 [1] Bioconductor
 BiocNeighbors          1.20.2     2024-01-07 [1] Bioconductor 3.18 (R 4.3.1)
 BiocParallel           1.36.0     2023-10-24 [1] Bioconductor
 BiocSingular           1.18.0     2023-10-24 [1] Bioconductor
 bitops                 1.0-7      2021-04-24 [1] RSPM (R 4.3.0)
 broom                  1.0.5      2023-06-09 [1] RSPM (R 4.3.0)
 car                    3.1-2      2023-03-30 [1] RSPM (R 4.3.0)
 carData                3.0-5      2022-01-06 [1] RSPM (R 4.3.0)
 class                  7.3-22     2023-05-03 [1] CRAN (R 4.3.1)
 cli                    3.6.2      2023-12-11 [1] RSPM (R 4.3.0)
 cluster                2.1.6      2023-12-01 [1] RSPM (R 4.3.0)
 codetools              0.2-19     2023-02-01 [1] CRAN (R 4.3.1)
 colorspace             2.1-0      2023-01-23 [1] RSPM (R 4.3.0)
 cowplot                1.1.2      2023-12-15 [1] RSPM (R 4.3.0)
 crayon                 1.5.2      2022-09-29 [1] RSPM (R 4.3.0)
 data.table             1.14.10    2023-12-08 [1] RSPM (R 4.3.0)
 DelayedArray           0.28.0     2023-10-24 [1] Bioconductor
 DelayedMatrixStats     1.24.0     2023-10-24 [1] Bioconductor
 deldir                 2.0-2      2023-11-23 [1] RSPM (R 4.3.0)
 dichromat              2.0-0.1    2022-05-02 [1] RSPM (R 4.3.0)
 digest                 0.6.34     2024-01-11 [1] RSPM (R 4.3.0)
 dotCall64              1.1-1      2023-11-28 [1] RSPM (R 4.3.0)
 dplyr                * 1.1.4      2023-11-17 [1] RSPM (R 4.3.0)
 edgeR                  4.0.7      2024-01-12 [1] Bioconductor 3.18 (R 4.3.1)
 ellipsis               0.3.2      2021-04-29 [1] RSPM (R 4.3.0)
 EnhancedVolcano      * 1.20.0     2023-10-24 [1] Bioconductor
 evaluate               0.23       2023-11-01 [1] RSPM (R 4.3.0)
 fansi                  1.0.6      2023-12-08 [1] RSPM (R 4.3.0)
 farver                 2.1.1      2022-07-06 [1] RSPM (R 4.3.0)
 fastDummies            1.7.3      2023-07-06 [1] RSPM (R 4.3.0)
 fastmap                1.1.1      2023-02-24 [1] RSPM (R 4.3.0)
 fitdistrplus           1.1-11     2023-04-25 [1] RSPM (R 4.3.0)
 forcats              * 1.0.0      2023-01-29 [1] RSPM (R 4.3.0)
 furrr                  0.3.1      2022-08-15 [1] RSPM (R 4.3.0)
 future                 1.33.1     2023-12-22 [1] RSPM (R 4.3.0)
 future.apply           1.11.1     2023-12-21 [1] RSPM (R 4.3.0)
 generics               0.1.3      2022-07-05 [1] RSPM (R 4.3.0)
 GenomeInfoDb           1.38.5     2023-12-28 [1] Bioconductor 3.18 (R 4.3.1)
 GenomeInfoDbData       1.2.11     2024-12-20 [1] Bioconductor
 GenomicRanges          1.54.1     2023-10-29 [1] Bioconductor
 ggbeeswarm             0.7.2      2023-04-29 [1] RSPM (R 4.3.0)
 ggforce                0.4.1      2022-10-04 [1] RSPM (R 4.3.0)
 ggplot2              * 3.5.1      2024-04-23 [1] RSPM (R 4.3.0)
 ggpubr                 0.6.0      2023-02-10 [1] RSPM (R 4.3.0)
 ggraph                 2.1.0      2022-10-09 [1] RSPM (R 4.3.0)
 ggrepel              * 0.9.5      2024-01-10 [1] RSPM (R 4.3.0)
 ggridges               0.5.5      2023-12-15 [1] RSPM (R 4.3.0)
 ggsignif               0.6.4      2022-10-13 [1] RSPM (R 4.3.0)
 globals                0.16.2     2022-11-21 [1] RSPM (R 4.3.0)
 glue                   1.7.0      2024-01-09 [1] RSPM (R 4.3.0)
 goftest                1.2-3      2021-10-07 [1] RSPM (R 4.3.0)
 gower                  1.0.1      2022-12-22 [1] RSPM (R 4.3.0)
 graphlayouts           1.0.2      2023-11-03 [1] RSPM (R 4.3.0)
 gridExtra              2.3        2017-09-09 [1] RSPM (R 4.3.0)
 gtable                 0.3.4      2023-08-21 [1] RSPM (R 4.3.0)
 gtools                 3.9.5      2023-11-20 [1] RSPM (R 4.3.0)
 hardhat                1.3.0      2023-03-30 [1] RSPM (R 4.3.0)
 hms                    1.1.3      2023-03-21 [1] RSPM (R 4.3.0)
 htmltools              0.5.7      2023-11-03 [1] RSPM (R 4.3.0)
 htmlwidgets            1.6.4      2023-12-06 [1] RSPM (R 4.3.0)
 httpuv                 1.6.13     2023-12-06 [1] RSPM (R 4.3.0)
 httr                   1.4.7      2023-08-15 [1] RSPM (R 4.3.0)
 ica                    1.0-3      2022-07-08 [1] RSPM (R 4.3.0)
 igraph                 1.6.0      2023-12-11 [1] RSPM (R 4.3.0)
 ipred                  0.9-14     2023-03-09 [1] RSPM (R 4.3.0)
 IRanges                2.36.0     2023-10-24 [1] Bioconductor
 irlba                  2.3.5.1    2022-10-03 [1] RSPM (R 4.3.0)
 jsonlite               1.8.8      2023-12-04 [1] RSPM (R 4.3.0)
 KernSmooth             2.23-22    2023-07-10 [1] RSPM (R 4.3.0)
 knitr                  1.45       2023-10-30 [1] RSPM (R 4.3.0)
 labeling               0.4.3      2023-08-29 [1] RSPM (R 4.3.0)
 later                  1.3.2      2023-12-06 [1] RSPM (R 4.3.0)
 lattice                0.22-5     2023-10-24 [1] RSPM (R 4.3.0)
 lava                   1.7.3      2023-11-04 [1] RSPM (R 4.3.0)
 lazyeval               0.2.2      2019-03-15 [1] RSPM (R 4.3.0)
 leiden                 0.4.3.1    2023-11-17 [1] RSPM (R 4.3.0)
 lifecycle              1.0.4      2023-11-07 [1] RSPM (R 4.3.0)
 limma                  3.58.1     2023-10-31 [1] Bioconductor
 listenv                0.9.0      2022-12-16 [1] RSPM (R 4.3.0)
 lmtest                 0.9-40     2022-03-21 [1] RSPM (R 4.3.0)
 locfit                 1.5-9.8    2023-06-11 [1] RSPM (R 4.3.0)
 lubridate            * 1.9.3      2023-09-27 [1] RSPM (R 4.3.0)
 magrittr               2.0.3      2022-03-30 [1] RSPM (R 4.3.0)
 mapproj                1.2.11     2023-01-12 [1] RSPM (R 4.3.0)
 maps                   3.4.2      2023-12-15 [1] RSPM (R 4.3.0)
 MASS                   7.3-60     2023-05-04 [1] CRAN (R 4.3.1)
 Matrix                 1.6-5      2024-01-11 [1] RSPM (R 4.3.0)
 MatrixGenerics         1.15.0     2024-12-20 [1] Github (Bioconductor/MatrixGenerics@ed066a2)
 matrixStats            1.2.0      2023-12-11 [1] RSPM (R 4.3.0)
 miloDE               * 0.0.0.9000 2024-12-20 [1] Github (MarioniLab/milODE@3f825b9)
 miloR                  1.10.0     2023-10-24 [1] Bioconductor
 mime                   0.12       2021-09-28 [1] RSPM (R 4.3.0)
 miniUI                 0.1.1.1    2018-05-18 [1] RSPM (R 4.3.0)
 munsell                0.5.0      2018-06-12 [1] RSPM (R 4.3.0)
 nlme                   3.1-164    2023-11-27 [1] RSPM (R 4.3.0)
 nnet                   7.3-19     2023-05-03 [1] CRAN (R 4.3.1)
 pals                 * 1.8        2023-08-23 [1] RSPM (R 4.3.0)
 parallelly             1.36.0     2023-05-26 [1] RSPM (R 4.3.0)
 parsnip                1.1.1      2023-08-17 [1] RSPM (R 4.3.0)
 patchwork              1.2.0      2024-01-08 [1] RSPM (R 4.3.0)
 pbapply                1.7-2      2023-06-27 [1] RSPM (R 4.3.0)
 pbmcapply              1.5.1      2022-04-28 [1] RSPM (R 4.3.0)
 pillar                 1.9.0      2023-03-22 [1] RSPM (R 4.3.0)
 pkgconfig              2.0.3      2019-09-22 [1] RSPM (R 4.3.0)
 plotly                 4.10.3     2023-10-21 [1] RSPM (R 4.3.0)
 plyr                   1.8.9      2023-10-02 [1] RSPM (R 4.3.0)
 png                    0.1-8      2022-11-29 [1] RSPM (R 4.3.0)
 Polychrome             1.5.1      2022-05-03 [1] RSPM (R 4.3.0)
 polyclip               1.10-6     2023-09-27 [1] RSPM (R 4.3.0)
 prodlim                2023.08.28 2023-08-28 [1] RSPM (R 4.3.0)
 progressr              0.14.0     2023-08-10 [1] RSPM (R 4.3.0)
 promises               1.2.1      2023-08-10 [1] RSPM (R 4.3.0)
 purrr                * 1.0.2      2023-08-10 [1] RSPM (R 4.3.0)
 qs                   * 0.25.7     2023-12-06 [1] RSPM (R 4.3.0)
 R6                     2.5.1      2021-08-19 [1] RSPM (R 4.3.0)
 randomForest           4.7-1.1    2022-05-23 [1] RSPM (R 4.3.0)
 RANN                   2.6.1      2019-01-08 [1] RSPM (R 4.3.0)
 RApiSerialize          0.1.2      2022-08-25 [1] RSPM (R 4.3.0)
 RColorBrewer           1.1-3      2022-04-03 [1] RSPM (R 4.3.0)
 Rcpp                   1.0.12     2024-01-09 [1] RSPM (R 4.3.0)
 RcppAnnoy              0.0.21     2023-07-02 [1] RSPM (R 4.3.0)
 RcppGreedySetCover     0.1.0      2018-01-24 [1] RSPM (R 4.3.0)
 RcppHNSW               0.5.0      2023-09-19 [1] RSPM (R 4.3.0)
 RcppParallel           5.1.7      2023-02-27 [1] RSPM (R 4.3.0)
 RCurl                  1.98-1.14  2024-01-09 [1] RSPM (R 4.3.0)
 readr                * 2.1.5      2024-01-10 [1] RSPM (R 4.3.0)
 recipes                1.0.9      2023-12-13 [1] RSPM (R 4.3.0)
 reshape2               1.4.4      2020-04-09 [1] RSPM (R 4.3.0)
 reticulate             1.34.0     2023-10-12 [1] RSPM (R 4.3.0)
 rlang                  1.1.3      2024-01-10 [1] RSPM (R 4.3.0)
 rmarkdown              2.25       2023-09-18 [1] RSPM (R 4.3.0)
 ROCR                   1.0-11     2020-05-02 [1] RSPM (R 4.3.0)
 rpart                  4.1.23     2023-12-05 [1] RSPM (R 4.3.0)
 rsample                1.2.0      2023-08-23 [1] RSPM (R 4.3.0)
 RSpectra               0.16-1     2022-04-24 [1] RSPM (R 4.3.0)
 rstatix                0.7.2      2023-02-01 [1] RSPM (R 4.3.0)
 rsvd                   1.0.5      2021-04-16 [1] RSPM (R 4.3.0)
 Rtsne                  0.17       2023-12-07 [1] RSPM (R 4.3.0)
 S4Arrays               1.2.0      2023-10-24 [1] Bioconductor
 S4Vectors              0.40.2     2023-11-23 [1] Bioconductor 3.18 (R 4.3.1)
 ScaledMatrix           1.10.0     2023-10-24 [1] Bioconductor
 scales                 1.3.0      2023-11-28 [1] RSPM (R 4.3.0)
 scattermore            1.2        2023-06-12 [1] RSPM (R 4.3.0)
 scatterplot3d          0.3-44     2023-05-05 [1] RSPM (R 4.3.0)
 scMisc               * 0.3.0      2024-12-20 [1] Github (mihem/scMisc@6b1e979)
 sctransform            0.4.1      2023-10-19 [1] RSPM (R 4.3.0)
 scuttle                1.12.0     2023-10-24 [1] Bioconductor
 sessioninfo          * 1.2.2      2021-12-06 [1] RSPM (R 4.3.0)
 Seurat               * 5.0.1      2024-12-20 [1] Github (fentouxungui/seurat@d2d8d60)
 SeuratObject         * 5.0.1      2023-11-17 [1] RSPM (R 4.3.0)
 shiny                  1.8.0      2023-11-17 [1] RSPM (R 4.3.0)
 SingleCellExperiment   1.24.0     2023-10-24 [1] Bioconductor
 sp                   * 2.1-2      2023-11-26 [1] RSPM (R 4.3.0)
 spam                   2.10-0     2023-10-23 [1] RSPM (R 4.3.0)
 SparseArray            1.2.3      2023-12-25 [1] Bioconductor 3.18 (R 4.3.1)
 sparseMatrixStats      1.13.4     2024-12-20 [1] Github (const-ae/sparseMatrixStats@4c6e814)
 spatstat.data          3.0-3      2023-10-24 [1] RSPM (R 4.3.0)
 spatstat.explore       3.2-5      2023-10-22 [1] RSPM (R 4.3.0)
 spatstat.geom          3.2-7      2023-10-20 [1] RSPM (R 4.3.0)
 spatstat.random        3.2-2      2023-11-29 [1] RSPM (R 4.3.0)
 spatstat.sparse        3.0-3      2023-10-24 [1] RSPM (R 4.3.0)
 spatstat.utils         3.0-4      2023-10-24 [1] RSPM (R 4.3.0)
 statmod                1.5.0      2023-01-06 [1] RSPM (R 4.3.0)
 stringfish             0.16.0     2023-11-28 [1] RSPM (R 4.3.0)
 stringi                1.8.3      2023-12-11 [1] RSPM (R 4.3.0)
 stringr              * 1.5.1      2023-11-14 [1] RSPM (R 4.3.0)
 SummarizedExperiment   1.32.0     2023-10-24 [1] Bioconductor
 survival               3.5-7      2023-08-14 [1] RSPM (R 4.3.0)
 tensor                 1.5        2012-05-05 [1] RSPM (R 4.3.0)
 tester                 0.1.7      2013-11-14 [1] RSPM (R 4.3.0)
 tibble               * 3.2.1      2023-03-20 [1] RSPM (R 4.3.0)
 tidygraph              1.3.0      2023-12-18 [1] RSPM (R 4.3.0)
 tidyr                * 1.3.0      2023-01-24 [1] RSPM (R 4.3.0)
 tidyselect             1.2.0      2022-10-10 [1] RSPM (R 4.3.0)
 tidyverse            * 2.0.0      2023-02-22 [1] RSPM (R 4.3.0)
 timechange             0.2.0      2023-01-11 [1] RSPM (R 4.3.0)
 timeDate               4032.109   2023-12-14 [1] RSPM (R 4.3.0)
 tweenr                 2.0.2      2022-09-06 [1] RSPM (R 4.3.0)
 tzdb                   0.4.0      2023-05-12 [1] RSPM (R 4.3.0)
 utf8                   1.2.4      2023-10-22 [1] RSPM (R 4.3.0)
 uwot                   0.1.16     2023-06-29 [1] RSPM (R 4.3.0)
 vctrs                  0.6.5      2023-12-01 [1] RSPM (R 4.3.0)
 vipor                  0.4.7      2023-12-18 [1] RSPM (R 4.3.0)
 viridis                0.6.4      2023-07-22 [1] RSPM (R 4.3.0)
 viridisLite            0.4.2      2023-05-02 [1] RSPM (R 4.3.0)
 withr                  2.5.2      2023-10-30 [1] RSPM (R 4.3.0)
 xfun                   0.41       2023-11-01 [1] RSPM (R 4.3.0)
 xtable                 1.8-4      2019-04-21 [1] RSPM (R 4.3.0)
 XVector                0.42.0     2023-10-24 [1] Bioconductor
 yaml                   2.3.8      2023-12-11 [1] RSPM (R 4.3.0)
 yardstick              1.2.0      2023-04-21 [1] RSPM (R 4.3.0)
 zlibbioc               1.48.0     2023-10-24 [1] Bioconductor
 zoo                    1.8-12     2023-04-13 [1] RSPM (R 4.3.0)

 [1] /opt/R/4.3.1/lib/R/library

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